TESpecificity

Species

Code	Species
Sbi	Sorghum bicolor
Shy	Saccharum hybrid (R570)
Sit	Setaria italica
Sof	Saccharum officinarum
Ssp	Saccharum spontaneum
Svi	Setaria viridis
Zma1	Zea mays

Each species has its own directory (Sbi/, Shy/, ...) with RUVr-corrected expression counts, a Salmon length reference, sample annotation, and this pipeline's output.

Pipeline

1. calculate_tau.py -- core pipeline: Tau, Extended Tau, and SPM per TE, per species.
2. te_classification_coverage.py -- which tested TE families are covered by the Order/Superfamily/Clade classification.
3. compare_te_classes_by_condition.py -- Fisher's-exact enrichment of TE classes among condition-specific TEs.
4. compare_te_specificity_across_species.py -- TE family specificity compared across species.
5. analyze_species_condition_proportions.py -- sample-count vs. specificity proportions per species/condition.

Steps 3-5 run independently on step 2's output.

Requirements

pip install -r requirements.txt

Usage

python3 calculate_tau.py
python3 compare_te_classes_by_condition.py
python3 compare_te_specificity_across_species.py
python3 analyze_species_condition_proportions.py
python3 te_classification_coverage.py

Each script also takes --help for its options.